NEW YORK, Dec 11 - Two leading bioinformaticists have issued a call to arms to their colleagues in response to Science’s decision to allow Celera to submit its genome data under special circumstances.
“Agitate. Let Science know you care,” write the letter’s authors, Ewan Birney of the European Bioinformatics Institute and Sean Eddy of the Howard Hughes Medical Institute and Washington University. “Even if we can’t change the deal with Celera, we can try to make sure it’s a one-time only deal that’s viewed as a Big Mistake.”
Under the terms of the agreement, which the parties announced Thursday, Science has agreed to allow Celera to submit its human genome sequence data to the journal while making the data available only on its website, not through a public international database such as Genbank, EMBL, or DDBJ. Previously, researchers have had to submit gene data to a public database before publication in Science.
Celera has agreed to make the published sequence data available free to academic users, but stipulated that researchers will have to agree in writing not to redistribute the data if they wish to download over one megabase. Commercial users also will be able to access this data, as long as they sign a material transfer agreement not to commercialize the results or redistribute the sequence.
Birney and Eddy decided to write the letter, " because it's a huge issue in bioinformatics, and from talking to [supervisory senior editor] Barbara Jasny at Science lastweek, I got the impression that Science had overlooked some serious problems with the deal they were proposing to Science ," Eddy told GenomeWeb.
because it's a huge issue in bioinformatics, and from talking to [supervisory senior editor] Barbara Jasny at Science lastweek, I got the impression that Science had overlooked some serious problems with the deal they were proposing to Science ," Eddy told GenomeWeb.
In their letter, Birney and Eddy said these restrictions on redistribution would present a significant obstacle to bioinformatics research.
“Bioinformatics research relies on open data with minimal legal encumbrances submitted to public databases,” wrote Birney and Eddy. “Without these databases there is no real substrate for bioinformatics research.”
Celera and Science have not yet hammered out the details for how the sequence data could be retrieved and used with minimal obstacles.
The bioinformaticists argue the Celera-Science agreement could set a precedent that would allow researchers to publish their databases under different material transfer agreements, making it impossible for researchers to access a single DNA database to do research, and forcing researchers to enter into a complex web of contracts to get access to data.
“You may need to get a legal review before you can publish the results of an analysis, if your analysis is large-scale and detailed enough that it could be reasonably interpreted as a ‘redistribution’ of the primary data,” Birney and Eddy warned.
In response to this letter, Jasny defended the journal’s decision as necessary and appropriate.
" First of all, in our view we are remaining true to our principles of access,” said Jasny. “We also strongly feel the alternative was that this data would not see the light of day except to a few subscribers. We felt that was a bad solution for the general public.”
But she also said Science is aware of concerns that bioinformaticists have about being able to publish work that involves large chunks of Celera’s data, and hopes there will be a way to make it possible for scientists to do this without running aground of the agreement.
“As far as the concerns of people doing whole genome annotations, [there] is ongoing discussion with Celera—on how to allow that,” Jasny said.
Meanwhile, other bioinformaticists have been responding to the letter--and not all of them agree with Birney and Eddy.
Bioinformatics consultant Nat Goodman called the publication agreement “a very statesmanlike compromise” between the interests of the scientific community and those of Celera.
" Science deserves credit for insisting on public access to the data,” Goodman said, noting that unencumbered access to intellectual property is not a requirement for publication. “If a company publishes analysis of a proprietary clone, they don’t have to give up the right to the commercial value of the clone,” he explained. “Because this is data, people feel differently.”
Shankar Subramaniam, a bioinformaticist at the University of California, San Diego, told GenomeWeb his primary concern stems from Celera’s use of public domain data to curate its proprietary database. “Certainly, they should return the raw sequence to the public," he said. “It’s reasonable to expect Celera to make the raw data available, though I understand they would want to protect the annotation.”
J. Robert Beck, vice president for information research and planning at Baylor College of Medicine, sees the agreement as a dangerous exception to the journal's standing policy of full disclosure. " Whether or not Celera makes it straightforward for researchers to get access to the data in this paper is secondary to the fact that this will make it easier to restrict access with regard to future advances, and I find this troubling,” he said.
Other bioinformaticists have been suggesting ways to do bioinformatics without violating the terms of the agreement. One researcher suggested in a bioinformatics forum that bioinformaticists could encode the data into aggregate script so that any “redistribution” that would occur through publishing the results would be redistribution of code, not data.
But Eddy said he thinks attempting to circumvent Celera's agreement with code would be a bad idea.
But Eddy said he thinks attempting to circumvent Celera's agreement with code would be a bad idea." I wouldn't want to expose myself to the legal liability," he said. " I don't think a court would look on that very favorably at all, if I'd signed a contract with Celera promising that I wouldn't redistribute the data."
Jasny also said that Science would be receiving a copy of the full sequence in escrow, on a DVD-ROM. This copy of the sequence would provide security for Celera’s assurance that it would uphold its end of the agreement.
“We will be keeping it safely with other AAAS valuables,” said Jasny.